| Read Background information on your Series 2 Forward Genetics Project at [[BISC219/F11:_Gene_Mapping_Info]]. Submit statement of Series 2 experimental question & goals. Outline (or create flow diagram) our experimental process including : Mutant Phenotype description compared to WT; Linkage Analysis; Mapping the Mutation to a chromosome and to a particular chromosomal location; Complementation Analysis; Defining the gene sequence and protein change through DNA sequence analysis; & Bioinformatics to find homologues and to determine if the mutation is new or previously characterized. Write a narrative summary of the investigation [[BISC219/F11: Assignment_Series2_Outline_Summary]].

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! Lab 3

! Lab 3

| Lab 4

| Lab 4

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| Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Linkage Testing work. Use only part of the template provided at [[Media:Series 2 Template for Crosses.ppt]] (Note that you will use and submit only through Linkage 2. (The Mapping part of the template will be used next week). Include a narrative description of this experimental design that you have drawn out on the template and summarize what you will be looking for in the results that will allow determination of the linkage group to which your mutated gene of interest belongs. Assignment information and rubric found at [[BISC219/F11: Assignment_Series2_Linkage Testing Crosses]]

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| Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Linkage Testing work. Use only part (through Linkage 2) of the template provided. (The Mapping part of the template will be used next week). Include a narrative description of this experimental design that you have drawn out on the template and summarize what you will be looking for in the results that will allow determination of the linkage group to which your mutated gene of interest belongs. Assignment information and rubric found at [[BISC219/F11: Assignment_Series2_Linkage Testing Crosses]]

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! Lab 4

! Lab 4

| Lab 5

| Lab 5

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| Explain complementation analysis in general and then explain specifically how you will use it to confirm and expand your linkage and mapping work. Draw out the crosses that you set up using the templates provided at [[Media:Complementation Template Crosses.ppt]]. Assignment information and rubric found at: [[BISC219/F11: Assignment_Series2_Complementation]]

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| Explain complementation analysis in general and then explain specifically how you will use it in this investigation. Draw out the crosses that you set up using the templates provided. Assignment information and rubric found at: [[BISC219/F11: Assignment_Series2_Complementation]]

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! Lab 8

! Lab 8

| Lab 9

| Lab 9

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| Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is described at [[BISC219/F11: Assignment_Series3_ Materials and Methods]]. Due at the beginning of Lab 9. Bring hard copies of the following journal articles to use during a science writing workshop and concept discussion in Lab9: Read the original 1998 paper by Fire and Mello published in ''Nature'' '''391''': 806-811 (Feb.19 1998) at [http://dx.doi.org/10.1038/35888 doi:10.1038/35888] ; Do your own library search to find and read a recent review article about RNAi in ''C. elegans''. Also read the 2002 Simmer ''et al.'' paper in ''Current Biology'' '''12''':1317-1319 explaining the ''rrf-3'' strain that we will use for our RNAi work at [http://dx.doi.org/10.1016/S0960-9822(02)01041-2 doi:10.1016/S0960-9822(02)01041-2 ]. These articles provide background information on how the mechanism of RNAi was worked out experimentally and will be helpful to you when you write the introduction section of your Series3 paper. Also read and bring a published journal article by Green et al. (2009) Impact of Cigarette Smoke Exposure on Innate Immunity: A ''Caenorhabditis elegans'' Model. PLoS ONE 4(8): e6860, found at [http://dx.doi.org/10.1371/journal.pone.0006860 doi:10.1371/journal.pone.0006860]. This study, like yours, uses reverse genetics to investigate gene function. Be prepared to use this paper in a discussion of the structure of science writing in Lab 9.

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| Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is described at [[BISC219/F11: Assignment_Series3_ Materials and Methods]]. Due at the beginning of Lab 9. Bring hard copies of the journal articles assigned to use during a science writing workshop and concept discussion in Lab9 and be prepared to lead the class discussion or summarize the major points of the article your group was assigned:

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These articles will provide helpful information when you write your Series3 paper. A good published journal article (that you need not read for content) by Green et al. (2009) Impact of Cigarette Smoke Exposure on Innate Immunity: A ''Caenorhabditis elegans'' Model. PLoS ONE 4(8): e6860, found at [http://dx.doi.org/10.1371/journal.pone.0006860 doi:10.1371/journal.pone.0006860] uses reverse genetics to investigate gene function. It may be a helpful model when you write some of your M&M section for your final paper.

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! Other

! Other

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| Exit Assessment participation. See First class conference for link and for instructions on how to receive your incentive points (2.5).

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| Exit Assessment participation. See Sakai Announcement for link and for instructions on how to receive your incentive points (2.5).

Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Linkage Testing work. Use only part (through Linkage 2) of the template provided. (The Mapping part of the template will be used next week). Include a narrative description of this experimental design that you have drawn out on the template and summarize what you will be looking for in the results that will allow determination of the linkage group to which your mutated gene of interest belongs. Assignment information and rubric found at BISC219/F11: Assignment_Series2_Linkage Testing Crosses

5

Lab 4

Lab 5

Explain complementation analysis in general and then explain specifically how you will use it in this investigation. Draw out the crosses that you set up using the templates provided. Assignment information and rubric found at: BISC219/F11: Assignment_Series2_Complementation

5

Lab 5

Lab 6

Diagram the expected results (genotype and phenotype)for the crosses and self-fertilization progeny in the Mapping work that you will do over the next several weeks by completing the templates provided. Make sure you highlight the progeny that will be used to continue each step of the process. Assignment information and rubric found at: BISC219/F11: Assignment_Series2_Mapping Crosses.

5

Lab 6

Lab 7

Analyze your mutant gene's DNA sequence using the instructions that you can download from Lab 6. Construct a Results and Discussion section, WITH A FIGURE, for this analysis. Assignment information and rubric found at: BISC219/F11: Assignment_Series2_DNA Sequencing

Convert all Series3 Protocols, performed so far, as Materials & Methods. This Assignment is described at BISC219/F11: Assignment_Series3_ Materials and Methods. Due at the beginning of Lab 9. Bring hard copies of the journal articles assigned to use during a science writing workshop and concept discussion in Lab9 and be prepared to lead the class discussion or summarize the major points of the article your group was assigned:

These articles will provide helpful information when you write your Series3 paper. A good published journal article (that you need not read for content) by Green et al. (2009) Impact of Cigarette Smoke Exposure on Innate Immunity: A Caenorhabditis elegans Model. PLoS ONE 4(8): e6860, found at doi:10.1371/journal.pone.0006860 uses reverse genetics to investigate gene function. It may be a helpful model when you write some of your M&M section for your final paper.

Construct figures/tables with properly formatted legends to illustrate the main findings of the RNAi part of your Series3:Reverse Genetics project. These figures are a draft of those that will be part of the results section of the research report you will write for Series3.